SMTL ID : 5hcn.1

GPN-loop GTPase Npa3 in complex with GMPPCP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x DAO: LAURIC ACID(Non-covalent)

DAO.1: 13 residues within 4Å: Chain A: V.138, N.143, F.149, N.152, M.153, A.156, C.157, F.171, W.185, F.189, L.215, F.218, L.222 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.149, A:A.156, A:F.189, A:L.215, A:F.218, A:F.218, A:L.222 Hydrogen bonds: A:N.143, A:N.152, A:W.185

1 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.2: 17 residues within 4Å: Chain A: M.10, A.11, G.12, S.13, G.14, K.15, T.16, T.17, G.108, N.172, K.173, D.175, V.176, S.228, S.229, F.230 Ligands: MG.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.12, A:S.13, A:G.14, A:K.15, A:T.16, A:T.17, A:T.17, A:D.39, A:D.39, A:N.172, A:K.173, A:K.173, A:S.229, A:F.230 Water bridges: A:K.15, A:K.15, A:T.16, A:T.16, A:T.16 Salt bridges: A:D.175 pi-Stacking: A:F.230 pi-Cation interactions: A:F.230

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: K.15, T.16 Ligands: GCP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.16, H2O.1, H2O.1, H2O.1

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: Q.20, R.44, P.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.44, A:R.44 GOL.5: 5 residues within 4Å: Chain A: K.178, F.181, E.184, W.185, D.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.143, A:K.178, A:F.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niesser, J. et al., Structure of GPN-Loop GTPase Npa3 and Implications for RNA Polymerase II Assembly. Mol.Cell.Biol. (2015)

Release Date

2016-01-13

Peptides

GPN-loop GTPase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GPN-loop GTPase 1

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